Save location and safe backup before updates
Quick answer
The Windows progression save is listed under %LOCALAPPDATA%\SpeciesUnknown\Saved\SaveGames\. Preserve a copy before making manual changes.
On this page
Locate the right files
Close the game before copying its saves. In Windows File Explorer, enter %LOCALAPPDATA%\SpeciesUnknown\Saved\SaveGames\. The community technical reference identifies SaveGame_Progress.sav as the progression file. Configuration is separately listed under Saved\Config\Windows\; a settings folder is not a substitute for the progression save.
Copy the existing folder to a separate backup location and label it with the game build and date. Keep the original untouched while troubleshooting. Check that the copied file exists before editing or replacing anything.
What a backup cannot promise
A local copy preserves the files you currently have. It does not guarantee compatibility with a later Early Access build or reverse a developer-directed progression reset. Steam Cloud participation also does not make every older state available on demand.
If an update changes progression, read the current official announcement before restoring an old save. Avoid launching repeatedly through a suspected conflict without first preserving both available copies. When requesting support, describe the build, whether Cloud was enabled, and the exact sequence that preceded the missing progress.